Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut

BMC Microbiology

Yumi Shimomura¹  Yoshihisa Wakita²  Yusuke Kitada³ 

[1] Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Hinode-machi, Tokyo, Japan;Frontier Laboratories for Value Creation, Sapporo Holdings Ltd., Shizuoka, Japan;Human Metabolome Technologies, Inc., Yamagata, Japan

关键词: Gut microbiome;    Metabolome;    Taxonomy;    16S amplicon sequencing;    Principal component analysis;   

DOI  :  10.1186/s12866-018-1311-8

学科分类：微生物学和免疫学

来源: BioMed Central

【 摘 要 】

16S rRNA gene amplicon sequencing analysis (16S amplicon sequencing) has provided considerable information regarding the ecology of the intestinal microbiome. Recently, metabolomics has been used for investigating the crosstalk between the intestinal microbiome and the host via metabolites. In the present study, we determined the accuracy with which 16S rRNA gene data at different classification levels correspond to the metabolome data for an in-depth understanding of the intestinal environment. Over 200 metabolites were identified using capillary electrophoresis and time-of-flight mass spectrometry (CE-TOFMS)-based metabolomics in the feces of antibiotic-treated and untreated mice. 16S amplicon sequencing, followed by principal component analysis (PCA) of the intestinal microbiome at each taxonomic rank, revealed differences between the antibiotic-treated and untreated groups in the first principal component in the family-, genus, and species-level analyses. These differences were similar to those observed in the PCA of the metabolome. Furthermore, a strong correlation between principal component (PC) scores of the metabolome and microbiome was observed in family-, genus-, and species-level analyses. Lower taxonomic ranks such as family, genus, or species are preferable for 16S amplicon sequencing to investigate the correlation between the microbiome and metabolome. The correlation of PC scores between the microbiome and metabolome at lower taxonomic levels yield a simple method of integrating different “-omics” data, which provides insights regarding crosstalk between the intestinal microbiome and the host.

【 授权许可】

CC BY